Align C4-dicarboxylate TRAP transporter small permease protein DctQ (characterized)
to candidate HSERO_RS04245 HSERO_RS04245 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07837 (227 letters) >FitnessBrowser__HerbieS:HSERO_RS04245 Length = 186 Score = 225 bits (574), Expect = 4e-64 Identities = 115/201 (57%), Positives = 138/201 (68%), Gaps = 18/201 (8%) Query: 2 LRILDRAEEVLIAALIATATVLIFVSVTHRFTLGFVADFVGFFRGHGMTGAAAAAKSLYT 61 +++LD EE LIA L+A AT +IFV+V HR+ G + L Sbjct: 1 MKLLDHLEEWLIAFLMAAATFIIFVAVVHRYASGLDIPW------------------LQD 42 Query: 62 TLRGINLVWAQELCIILFVWMAKFGAAYGVRTGIHVGIDVLINRLDAPKRRFFILLGLGA 121 L IN+ WAQELCI +FVWMAKFGAAYGVRTGIHVG+DVLINRL+ P R F+L GL A Sbjct: 43 QLIQINMSWAQELCIFMFVWMAKFGAAYGVRTGIHVGVDVLINRLNTPWRNKFVLFGLFA 102 Query: 122 GALFTGIIATLGANFVLHMYHASSTSPDLELPMWLVYLAIPMGSSLMCFRFLQVAFGFAR 181 GALFTGI+ T GA FV + STS +E+PMW+VYLA+P+GS LMCFRFLQVA+ F R Sbjct: 103 GALFTGIVGTFGAEFVYDIAQHDSTSEVMEVPMWIVYLAVPLGSYLMCFRFLQVAWNFHR 162 Query: 182 TGELPHHDHGHVDGVDTENEG 202 TGELP HDH HV+G+D E G Sbjct: 163 TGELPKHDHAHVEGLDEETSG 183 Lambda K H 0.328 0.143 0.442 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 150 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 227 Length of database: 186 Length adjustment: 21 Effective length of query: 206 Effective length of database: 165 Effective search space: 33990 Effective search space used: 33990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory